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ff19SB: Amino-Acid Specific Protein Backbone Parameters Trained Against Quantum Mechanics Energy Surfaces in Solution

Chuan Tian, Koushik Kasavajhala, Kellon Belfon, Lauren Raguette, He Huang, Angela Migues, John Bickel, Yuzhang Wang, Jorge Pincay, Qin Wu, Carlos Simmerling

Version 1 posted 17 June 2019

2,725

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1

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Biological and Medicinal Chemistry

Working Paper

Simulating Chalcogen Bonding Using Molecular Mechanics: A Pseudoatom Approach to Model Ebselen.

Thomas Fellowes, JONATHAN WHITE

Version 2 posted 05 May 2021

683

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Theoretical and Computational Chemistry

Working Paper

Accounting for the Central Role of Interfacial Water in Protein-Ligand Binding Free Energy Calculations

Ido Ben-Shalom, Zhixiong Lin, Brian Radak, Charles Lin, Woody Sherman, Michael K. Gilson

Version 1 posted 20 July 2020

595

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1

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Theoretical and Computational Chemistry

Working Paper

Blinded Prediction of Protein-Ligand Binding Affinity Using Amber Thermodynamic Integration for the 2018 D3R Grand Challenge 4

Junjie Zou, Chuan Tian, Carlos Simmerling

Version 1 posted 24 June 2019

1,095

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Theoretical and Computational Chemistry

Working Paper

Systematic comparison of Amber and Rosetta energy functions for protein structure evaluation.

Aliza Rubenstein, Kristin Blacklock, Hai Nguyen, David Case, Sagar Khare

Version 2 posted 04 April 2018

1,602

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Theoretical and Computational Chemistry

Working Paper

Validation of AMBER/GAFF for Relative Free Energy Calculations

Lin Song, Tai-Sung Lee, Chun Zhu, Darrin M. York, Kenneth M. Merz Jr.

Version 1 posted 04 February 2019

1,810

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2

Citations

Biological and Medicinal Chemistry

Working Paper

A Fast Implementation of the Nudged Elastic Band Method in AMBER

Delaram Ghoreishi, David Cerutti, Zachary Fallon, Carlos Simmerling, Adrian Roitberg

Version 1 posted 18 June 2019

808

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Theoretical and Computational Chemistry

Working Paper

Short-Range Imbalances in the AMBER Lennard-Jones Potential for (Deoxy)Ribose…Nucleobase Lone-pair…π Contacts in Nucleic Acids.

Klaudia Mrazikova, Jiri Sponer, Vojtech Mlynsky, Pascal Auffinger, Holger Kruse

Version 1 posted 15 September 2021

282

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Theoretical and Computational Chemistry

Working Paper

Accurate Free Energy Calculation via Multiscale Simulations Driven by Hybrid Machine Learning and Molecular Mechanics Potentials

Xujian Wang, Junmei Wang, Xiongwu Wu, Bernard Brooks

Version 1 posted 08 November 2024

293

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Theoretical and Computational Chemistry

Working Paper

Influence of non-protein amino-acid mimosine in peptide conformational propensities from novel Amber force field parameters

Asier Urriolabeitia, David De Sancho, Xabier López

Version 1 posted 09 November 2021

178

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17 results in Amber in Keywords: Amber

ff19SB: Amino-Acid Specific Protein Backbone Parameters Trained Against Quantum Mechanics Energy Surfaces in Solution

Simulating Chalcogen Bonding Using Molecular Mechanics: A Pseudoatom Approach to Model Ebselen.

Accounting for the Central Role of Interfacial Water in Protein-Ligand Binding Free Energy Calculations

Blinded Prediction of Protein-Ligand Binding Affinity Using Amber Thermodynamic Integration for the 2018 D3R Grand Challenge 4

Systematic comparison of Amber and Rosetta energy functions for protein structure evaluation.

Validation of AMBER/GAFF for Relative Free Energy Calculations

A Fast Implementation of the Nudged Elastic Band Method in AMBER

Short-Range Imbalances in the AMBER Lennard-Jones Potential for (Deoxy)Ribose…Nucleobase Lone-pair…π Contacts in Nucleic Acids.

Accurate Free Energy Calculation via Multiscale Simulations Driven by Hybrid Machine Learning and Molecular Mechanics Potentials

Influence of non-protein amino-acid mimosine in peptide conformational propensities from novel Amber force field parameters

17 results in Keywords: Amber